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What Is The Structure Of A Protein?

What is the structure of a protein? Here`s a question for the scientist in you that needs an answer.

What Is The Structure Of A Protein

What Is a Protein?

A protein is a macromolecular organic substance that is formed by simple or complex amino-acid chains. Proteins can be found in the cells of all living organisms in more than 50% of the dry weight. All proteins are polymers of amino acids, where their sequence is encoded by a gene. Each and every protein has its very own unique amino acid sequence that is determined by the nucleotide sequence of the gene.

What Is the Structure of a Protein?

The elucidation of the protein structure has been among the main issues of applied biochemistry. Every native protein is a complex 3-dimensional edifice whose conformation depends on the spatial disposition of the polypeptide chains from which it`s formed. The spatial orientation of the polypeptide chains is known as conformation.

Compared with nucleic acids, a protein is much more elastic in structure. It has lots of biochemical and biological roles, especially in the cell, as structural elements, enzymatic components. A lot of the protein metabolism stages are controlled and regulated by enzymes.

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The forces which will establish the protein structure are of a covalent and non-covalent type.

  • Van der Waals forces: a non-planetary force which expresses the universal attraction between 2 neighboring atoms. In fact, the Van der Waals forces are weaker than covalent forces, the distances being greater than 3 – 4 A. Still, by cumulation, due to the large number of interactions, these particular forces might gain a quantitative aspect.
  • Hydrophobic forces: negative non-covalent forces, due to the presence of hydrophobic chains in aqueous solutions. These forces are among those that determine to a large extent the structure of proteins.
  • Electrostatic forces: they determine especially interactions between 2 peptide chains with distinct charges. Water and dissolved ions can be “screens” for this type of interactions, therefore reducing their distances and strength to which they might operate.
  • The dipole moment: caused by distant pairs of distances at greater distances, leads to the emergence of an electric field. It`s frequently used by proteins to attract and position substrates or products.
  • Hydrogen bonds: they are dipole-dipole interactions that involve hydrogen polar molecules. Hydrogen linkages don`t usually contribute to the net protein stabilization because the same hydrogen bonding group with another protein molecule can form hydrogen bonds with denatured water.
  • Distances and angles of covalent bonds: they are actually the main properties which cause the maintenance of protein molecules linked to each other.

Proteins might be constituted by a single polypeptide or complexes of 2 or more polypeptides. Depending on the type and nature of association, 2 or more polypeptide chains might e distinguished. The pairing of 2 identical polypeptides forms a homodimer. The combination of 2 different polypeptides forms a hetero-dimer. The complex formed by 3 polypeptides is known as trimer, 4 polypeptides as tetramer, and so forth. Often, there are used Greek symbols to describe the composition of the polypeptides, but this doesn`t mention anything about the protein structure, as you can notice below.

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Subunit Organization Composition Example
ab The protein consists of 2 separate polypeptide chains, each with another amino acid sequence, heterodimer Insulin

Chain “A” has 21 amino acids
Chain ‘B’ has 30 amino acids

a2 The protein consists of 2 separate but identical polypeptide chains, therefore homodimer Lambda phage Cro

Each polypeptide chain has 66 amino acids

abg The protein consists of 3 separate and distinct polypeptide chains, thus heterotrimer Chymotrypsin

Chain A has 13 amino acids

Chain b has 132 amino acids

Chain g has 97 amino acids

a2b2 The protein consists of 4 separate and distinct polypeptide chains, but 2 by 2 identical, so a homodimer dimer g-Globulin

Chain a has 214 amino acids
Chain b has 446 amino acids

 

When analyzing peptides by acid hydrolysis, generally with 6N boiling hydrochloric acid, the proportion of each amino acid in a polypeptide can be quantitatively determined. Still, there`re some issues related to this methods of analyzing the quantitative protein structure, meaning that tryptophan is destroyed, asparagines and glutamine are transformed into aspartic acid and glutamic acid, the aspartic acid and aspartine intake couldn`t be differentiated., and the same when glutamic acid and glutamine are concerned. Consequently, the percentage of amino acids in a protein can be determined, as exemplified in the table below.

Amino acid Concentration following hydrolysis (“n” moles) Normalized concentration (moles) Probable composition
Ala 570 12,7 13
Cys 58 1,3 1
Asx 400 8,9 9
Glx 690 15,3 15
Phe 300 6,7 7
Gly 520 11,6 12
His 410 9,1 9
Ile 275 6,1 6
Lys 725 16,1 16
Leu 700 15,6 16
Met 110 2,4 2
Pro 180 4,0 4
Arg 120 2,7 3
Ser 240 5,3 5
Thr 97 2,2 2
Val 255 5,7 6
Tyr 45 1,0 1
Total amino acids: 127

 

1. Primary Structure

The primary structure is the amino acid sequence encoded in the deoxyribonucleic acid (DNA). It consists of strong covalent peptide forces that are rarely broken in food processing operations.

2. Secondary Structure

The local structures are structures of regional structural periodicity encountered in a variety of types of proteins. There are 3 types of proposed for such representations:

A. a-helix, (propeller a)a-helix

Spiral pattern resulting from coiling the polypeptide chain around an imaginary cylinder, either clockwise, a-right helix, or counterclockwise, a-helix of the left. – Read more!

B. Folded patterns which can occur in 2 variants. The first case is the parallel pattern of folded structures, characteristic of the structure of the b-keratin structure.Folded patterns

C. The anti-parallel pattern of folded structures, characteristic of silk fibrous, wherein the peptide ends are located one in front of the other.anti-parallel pattern

3. Tertiary Structure

Secondary structures don`t sufficiently conceal hydrophobic structures and tend to become more of a detail than an intrinsic force. Such a structure is needed so that the hydrophobic parts are even better hidden, the hydrophilic parts being exposed. The “packaging” of the biopolymer so that they hydrophilic parts are exposed and the hydrophobic parts as “hidden” can be realized naturally by what has been designed as the tertiary structure.

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The tertiary structure represents a level of organization resulting from interactions between amino acid residues present in polypeptides. It`s suggested that each and every propeller can turn around another so that conglomerates with a complex molecular architecture resembling a 7-core twisted yarn.

The maintenance of tertiary structures is achieved through the forces of attraction that arise between the radicals in the polypeptide chains. The nature of these forces can be of the type:

  • Hydrogen forces between phenolic (tyrosine) OH groups (serine) with carboxyl groups.
  • Ionic bonds which occur between carboxyl groups of dicarboxylic amino acids and amino groups of diamine amino acids when the spacing between groups is between 2-3 A.
  • Van der Waal apolar connections.

This diversity of linkages in protein biopolymer structures determines their lability at a whole range of external or cellular factors. Destruction, even to a limited extent, of this complex organization leads to the loss of the biological properties involved. However, extremely small changes can be made to such structures, for example by adsorption of a compound with a simple molecular weight, a phenomenon called the allosteric effect, which is particularly important in enzyme activity.

The secondary and tertiary structure allowed the proteins to be classified into 2 major classes:

  • Fibril proteins.
  • Globular proteins.

Besides these, there would still be a class with undefined structure. – More details!

Fibrilled proteins have a threadlike structure constituted by linear chains, having supportive and mechanical resistance functions. Representatives of this class are proteins, like myosin, hair keratin, silk fibrous.

Globular counterparts to the name, have an ellipsoidal cylindrical tubular shape with a length exceeding 2 – 6 times the diameter. Representatives of this category are found almost in all liquids in the human body.

4. Quaternary Structure

The quaternary structure of proteins is a super way of organizing and aggregating the polypeptide chains which are accomplished by the intervention of the same forces as in the formation of previous structures, but interactions now refer to different chains. The most cited example is hemoglobin, the oxygen-carrying protein in the blood. Its structure consists of 4 polypeptide sequences and 4 prostatic groups, known as hem, which interact with each other and form the global structure.hemoglobin

Image courtesy of mun.ca
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